FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: 9Y812
Calculation Name: 1L2Y-A-MD56-31600ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-13
Reference:
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | No |
| Water | No |
| Procedure | Manual calculation |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 10 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -22902.12757 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18299.907379 |
| FMO2-HF: Total energy | -4602.22019 |
| FMO2-MP2: Total energy | -4615.621543 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
"| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(:1:GLN )
Summations of interaction energy for
fragment #1(:1:GLN )
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| -49.274 | -47.924 | 19.206 | -9.65 | -10.904 | -0.077 |
Interaction energy analysis for fragmet #1(:1:GLN )
| frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | 3 | GLN | 0 | 0.036 | 0.013 | 3.884 | 1.234 | 2.592 | -0.010 | -0.648 | -0.701 | -0.001 | |
| 4 | 4 | GLN | 0 | 0.067 | 0.039 | 6.726 | 0.917 | 0.917 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.051 | -0.025 | 2.435 | -17.448 | -13.237 | 3.340 | -2.996 | -4.555 | -0.030 | |
| 6 | 6 | GLN | 0 | 0.020 | 0.015 | 4.570 | -0.739 | -0.662 | -0.001 | -0.013 | -0.062 | 0.000 | |
| 7 | 7 | GLN | 0 | 0.052 | 0.021 | 1.787 | -14.191 | -18.648 | 15.877 | -5.968 | -5.451 | -0.046 | |
| 8 | 8 | GLN | 0 | -0.024 | -0.010 | 4.469 | 0.943 | 1.104 | 0.000 | -0.025 | -0.135 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.009 | -0.010 | 6.279 | 0.268 | 0.268 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.932 | -0.941 | 9.446 | -20.258 | -20.258 | 0.000 | 0.000 | 0.000 | 0.000 |